Contacts of the helix formed by residues 425 - 430 (chain J) in PDB entry 1FPY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 425 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421J LEU 3.2 15.8 + - - +
422J ASP* 2.7 45.3 + - - +
423J LEU 2.5 13.7 + - - +
424J ASP* 1.3 72.4 - - - +
426J GLU* 1.3 73.8 + - - +
427J PHE 3.4 0.4 - - - -
428J LEU* 3.1 20.7 + - - +
429J LYS* 3.4 25.6 + - + +
436J ASP* 3.1 36.5 + - - +
439J ILE* 4.0 20.3 - - + +
440J ASP* 3.0 39.4 + - - -
443J ILE* 4.4 3.8 - - - +
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Residues in contact with GLU 426 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423J LEU 4.9 4.9 - - - +
424J ASP* 3.1 5.1 - - - +
425J ARG* 1.3 85.2 - - + +
427J PHE* 1.3 63.1 + - - +
428J LEU 3.0 1.9 + - - -
429J LYS* 3.0 48.1 + - - +
430J ALA* 3.5 9.4 + - - +
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Residues in contact with PHE 427 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304J HIS* 3.5 39.7 - + + +
307J ALA* 4.2 9.4 - - + -
308J ILE* 4.5 7.0 - - + -
373J ALA* 3.7 3.8 - - + -
376J MET* 3.6 16.0 - - - +
377J ALA* 3.4 44.2 - - + -
380J ASP* 4.0 20.9 - - + +
424J ASP* 3.0 39.6 + - - -
426J GLU* 1.3 77.4 - - - +
428J LEU* 1.3 93.3 + - + +
430J ALA* 3.5 17.8 - - - +
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Residues in contact with LEU 428 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307J ALA* 5.3 1.6 - - + +
311J LEU* 5.6 2.0 - - + -
373J ALA* 3.9 21.5 - - + -
376J MET* 3.7 17.5 - - + +
421J LEU* 3.5 32.3 - - + -
425J ARG* 3.1 10.7 + - - +
426J GLU 3.0 1.2 - - - -
427J PHE* 1.3 121.7 - - + +
429J LYS* 1.3 59.6 + - - +
430J ALA 3.1 10.0 + - - +
433J VAL* 3.6 3.8 - - - +
434J PHE* 3.0 56.8 + - + +
439J ILE* 4.2 4.3 - - + -
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Residues in contact with LYS 429 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425J ARG* 3.5 29.9 - - + +
426J GLU* 3.0 36.7 + - - +
428J LEU* 1.3 72.6 - - - +
430J ALA* 1.3 68.3 + - - +
432J GLY* 2.9 18.9 + - - -
434J PHE 3.1 20.1 - - - +
435J THR* 4.8 1.8 - - - +
436J ASP* 3.0 41.4 + - - +
439J ILE* 4.2 10.8 - - + -
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Residues in contact with ALA 430 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J TYR* 3.6 25.6 - - + +
376J MET* 3.4 5.1 - - + +
383J LYS* 5.7 3.4 - - - +
426J GLU 3.5 6.8 + - - +
427J PHE* 3.5 20.9 - - - +
428J LEU 3.1 0.6 - - - -
429J LYS* 1.3 78.8 - - - +
431J GLY* 1.3 60.7 + - - +
432J GLY 2.9 5.9 + - - -
433J VAL* 3.1 18.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il